v0.2.2

[0.2.2] (04 Apr 2023)

• e1159c4 - Add V4.1 modified base models
• dd389f1 - Add ability to load POD5/FAST5 files recursively, remove the runners flag
• 5a55416 - Fix bug whereby the last read was ignored for read lists not terminated by a newline character
• 1c7988a - Performance improvements to Stereo Basecalling with better batch size selection
• 27c8a2e - Upgrade to Pod5 v0.1.13 which allows loading large files on vmem-limited systems
• 3a9bb7a - Incorporate improvements in Koi which give more predictive QV Scores
• 6896f09 - Fixes to dorado duplex basespace
• 1079b75 - Upgrade to Torch 2.0 and Cuda 11.8
• bcfd64d - If a Stereo model is not available for duplex basecalling, download it automatically
• 8b90643 - Improve Dorado startup time when using POD5 files by getting ReadGroup information from metadata tables
• e86e970 - Use jemalloc to override allocator on Linux
• 4d6a898 - Enable Stereo Duplex on M1
• db097be - Make metal stereo conv1 kernel available
• 17d97d3 - Make MetalModel capable of handling > 1 input channel (Required for Stereo Duplex)
• 6d5f07f - Fix memory leak in getting read groups
• 3e3b21a - Remove deprecated use of FindCUDA and show real location of found toolkit
• ff80a9f - Improvements to Mk1C performance
• 35dcb65 - Fix meaning of TLEN in SAM output
• 7f13113 - Add support for arbitrary messages in Dorado pipelines
• a93ae2c - Addition of a progress bar for basecalling
• a93ae2c - Solve bug which was occuring when a read had no mod base context hits
• 22a3140 - Refactoring of Dorado pipeline system to Add AsyncQueue and use it in ReadSink/Nodes
• 824459e - Add "cuda:auto" as alternative to "cuda:all" when selecting a compute accelerator device on CLI
• d0c9387 - Store reads raw data internally in fp16 format
• 6cd8170 - Switch post-ScalerNode raw_data to float16